A team member records where his team collects rock sediment samples.
Devlin A. Gandy
By Elizabeth Pennisi
When scientists need ancient DNA, they usually have to drill into their teeth or bones – a process that can destroy delicate, sometimes irreplaceable, samples. And that’s assuming they have teeth or bones in the first place.
Now, researchers have shown that they can recover not only high-quality antique DNA from dirt, but also close approximations of the entire genome. The samples in question – from a cave floor in northern Mexico – not only reveal another way to obtain such genetic material, but also help clarify the history of ice bears in North America.
The approach is a “huge breakthrough” for the ancient DNA field, says Anna Linderholm, an archaeologist at Texas A&M University College Station who was not involved in the work. “We only scratch the surface of what is possible when we recover ancient DNA from sediment.”
For the new study, molecular paleoecologist Mikkel Winther Pedersen of the GLOBE Institute at the University of Copenhagen reviewed the Chiquihuite Cave in northern Mexico. Since 2012, he and colleagues have discovered stone tools dating back about 30,000 years, and the team was curious about other inhabitants of the site, including ancient bears. The researchers took sediment samples at different levels of the cave floor, recovering DNA from 48 of them.
Instead of simply focusing on obtaining mitochondrial DNA – the small amount of genetic material present in cell centers – as previous studies of DNA in the soil have done, scientists have sequenced all the DNA in each sample. . To do this, they took advantage of techniques that make it possible to decipher billions of bases – or letters – of DNA in just a few days, and developed computer software to manage and analyze all that data. As part of the analysis, they compared the sequenced fragments with the bear’s DNA already in public databases.
From mitochondrial DNA, the researchers were able to determine that black bears (American bear) had long lived in the cave region – at least 3000 years.
Researchers explored the Chiquihuite Cave in northern Mexico to learn more about bears.
Devlin A. Gandy
Nuclear DNA analysis was more difficult because the bear’s genome is billions of bases long, and the fragments were at least the other thousands of bases. So the team put these fragments together and assessed how much of the genome they had, matching soil-derived DNA with existing bear DNA.
Finally, the researchers compiled harsh genomes from three black bears and what turned out to be a giant short-faced bear (we Arctodus), a best-known extinct fossil species in Canada. Pedersen calls his sequenced DNA “environmental genomes” to differentiate them from whole genomes now commonly obtained from living microbes and other organisms.
Researchers didn’t really know how bears went in the last ice age and what happened when the planet warmed again. But comparing the ancient genomes of the black bear with the genomes of the same species in North America, Pedersen’s team found that as the ice disappeared in North America, some black bears headed north to Alaska. Others are paired with black bears from the west, and their descendants later populate the southwestern United States, the team said today in Current biology.
Scientists do not know exactly when these expansions took place in ice-free areas, but only when the world warmed up 12,000 years ago. Some of these bears from the east crossed with other black bears from Alaska and migrated to another part of Alaska. Knowing the relationships between bears that live in different places can be important for conservation efforts, says Pedersen.
Rather than providing information about the history of bears in North America, the paper is also “proof of the concept,” says Ron Pinhasi, a physical anthropologist at the University of Vienna who has been studying ancient DNA for 10 years. it also sequences genomes from ancient soils. “They show how it is possible to analyze ancient DNA from environmental samples in a similar way, as is currently done for DNA from fossil remains.”
In other words, pay attention to several genomes in the old dirt.